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- EMDB-4995: Subtomogram average of a part of the rabies lyssavirus ribonucleo... -

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Entry
Database: EMDB / ID: EMD-4995
TitleSubtomogram average of a part of the rabies lyssavirus ribonucleoprotein
Map data
SampleRabies virus:
virus
Biological speciesRabies virus
Methodsubtomogram averaging / cryo EM / Resolution: 15 Å
AuthorsRiedel C / Vasishtan D / Prazak V / Ghanem A / Conzelmann K-K / Ruemenapf T
CitationJournal: Sci Rep / Year: 2019
Title: Cryo EM structure of the rabies virus ribonucleoprotein complex.
Authors: Christiane Riedel / Daven Vasishtan / Vojtěch Pražák / Alexander Ghanem / Karl-Klaus Conzelmann / Till Rümenapf /
Abstract: Rabies virus is an important zoonotic pathogen. Its bullet shaped particle contains a helical nucleocapsid. We used cryo-electron tomography and subsequent subtomogram averaging to determine the ...Rabies virus is an important zoonotic pathogen. Its bullet shaped particle contains a helical nucleocapsid. We used cryo-electron tomography and subsequent subtomogram averaging to determine the structure of its ribonucleoprotein. The resulting electron density map allowed for confident fitting of the N-protein crystal structure, indicating that interactions between neighbouring N-proteins are only mediated by N- and C-terminal protruding subdomains (aa 1-27 and aa 355-372). Additional connecting densities, likely stabilizing the ribonucleoprotein complex, are present between neighbouring M-protein densities on the same helical turn and between M- and N-protein densities located on neighbouring helical turns, but not between M-proteins of different turns, as is observed for the related Vesicular stomatitis virus (VSV). This insight into the architecture of the rabies virus nucleocapsid highlights the surprising structural divergence of large biological assemblies even if the building blocks - here exemplified by VSV M- and N-protein - are structurally closely related.
DateDeposition: May 22, 2019 / Header (metadata) release: May 29, 2019 / Map release: Jul 10, 2019 / Update: Jul 17, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4995.map.gz / Format: CCP4 / Size: 844.7 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.35 Å/pix.
x 60 pix.
= 201.12 Å
3.35 Å/pix.
x 60 pix.
= 201.12 Å
3.35 Å/pix.
x 60 pix.
= 201.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.352 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum0.3004837 - 10.78492
Average (Standard dev.)4.2021585 (±0.9374101)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 201.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.3523.3523.352
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z201.120201.120201.120
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean0.30010.7854.202

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Supplemental data

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Sample components

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Entire Rabies virus

EntireName: Rabies virus / Number of components: 1

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Component #1: virus, Rabies virus

VirusName: Rabies virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Rabies virus
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 7079
3D reconstructionResolution: 15 Å / Resolution method: FSC 0.143 CUT-OFF

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